#63 ~ September 2011
Contents
News – Updates & meetings
Scripts Spotlight – Gated analysis
Spike2 – Individual channel colours
Spike2 Script – Export triggered data to Matlab
Signal – Dynamic clamp models
Signal Script – Measurement of AP half-heights
Did you know…? – Channel ordering
Recent questions – Triggering 1902 input clamp prior to Magstim
News
US Training Days: Thursday 10th and Friday 11th November
These training days will take place at the Holiday Inn Rosslyn at Key Bridge, 1900 N Fort
Myer Drive, ARLINGTON, VA just prior to the Society for Neuroscience meeting in
Washington, DC. The days are suitable for both existing and prospective users so join us
and learn how to make the most of Spike2 and Signal for your individual data acquisition
and analysis requirements.
•
Covers all the major features of Spike2 and Signal
•
In-depth tutorials take you from recording data through to advanced
analysis techniques
•
Optional workshop sessions allow you to discuss specific questions with
CED staff in a small group environment
Attendance is limited so please register early to reserve your place on the appropriate
course.
Future meetings and events
Spanish Neuroscience Society
University of Salamanca,
Salamanca, Spain
September 28th – 30th 2011
Society for Neuroscience 2011
Booth 2238 - Walter E. Washington Convention Center,
Washington, DC, USA
November 12th – 16th 2011
Australian Neuroscience Society 2012
Jupiters Hotel,
Gold Coast, QLD, Australia
January 29th – February 1st 2012
Latest versions of Spike2 and Signal
Updates for Spike2 and Signal are available from the CED downloads page, or by
clicking on the links in the table below. Demonstration versions of the latest software are
also available.
Spike2 downloads
Released
Signal downloads
Released
Spike2 version 7.07
07/11
Signal version 5.03
09/11
Spike2 version 6.16
03/11
Signal version 4.09
08/11
Spike2 demo
Signal demo
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Scripts Spotlight
Gated analysis
One of the first things that you learn as a new Spike2 user is how to take measurements
over a time range by bracketing it with cursors and using the Cursor Regions dialog.
This is all well and good but can become tedious if you have multiple time ranges to
analyse. There are several scripts in the Spike2 scripts folder that can speed things up.
TimeRanges.s2s allows you to mark multiple time ranges of interest as coloured bars
using the State channel draw mode. You can then use WMeasure.s2s to take your
chosen cursor regions type measurement (sum, mean, peak-to-peak etc.) repeatedly at
fixed intervals over a selected time range or only during the marked time ranges, i.e.,
gated by the range marker channel. The results are tabulated in the log view and can be
pasted to a spreadsheet. You also have the option to plot the results as an additional
channel in the data file.
Similarly, GatedPower.s2s allows you to generate a power spectrum based only on the
data within marked time ranges. This script also has an option to overlap FFT blocks so
that all of the raw data is included in the spectrum. This option is given because power
spectra are performed on successive time slices or epochs with a duration determined by
the sample rate and the chosen FFT size (i.e. 256, 512, 1024 etc… samples). Partial
epochs cannot be analysed. So, if the duration of a range is not an exact multiple of the
epoch duration, then we have to make a choice between ignoring the data in the partial
epoch at the end of the time range or, overlapping the epochs for a perfect fit. In practice
we aim not for minimum overlap but an overlap of close to fifty percent.
Each of these scripts generates a hotkey on the Script Bar when you run them for the
first time. These buttons allow you to quickly flip from one script to the other. You will find
user guides in the comments section at the top of the script file. Users of Spike2 v7 will
find these scripts in the scripts folder.
If you have any questions please contact [email protected]
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Q.
I’d like to set-up my data-file so that different channels are displayed in different
colours for easy identification.
A.
You can set individual colours for almost all types of data, channel and view in
Spike2. Click on the colour palette icon in the main Spike2 toolbar or select
Change colours… from the View menu to access the Set colours dialog.
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Set colours dialog
With a data file open, the Set colours dialog will display a list of the channels
in the file. The drop-down menu can then be used to select the different channel
elements such as primary, secondary and background colour for the listed
channels. Click on the name of the channel you want to change and then click a
colour in the palette to apply it to the selected channel element.
Set custom colours
The available colours in the palette can be changed by double clicking on a
colour. This opens a new dialog where you can select Basic colours to add to the
palette or define your own Custom colours with user-definable settings for Hue
Saturation, Luminescence or RGB ratio.
Processed EMG data duplicated with primary and background colours
changed
Channel colour settings are stored in the resource file that is associated with the
data file. Resource files have the same name as the data file and are stored in
the same location with the extension .S2R. You can apply colour settings from
one file to other data files using the File menu Resource Files > Apply
Resource Files… option.
Scripts: Spike2
Q.
A.
I would like to export a channel of waveform data to Matlab for external analysis.
The problem I’m having is that my original recording took place over a long
period, making the data file, and associated Matlab file, rather large. Is there any
way to export just sections of the waveform, perhaps based on a stimulus trigger
recorded as an event channel?
The script, TrigDataExport.s2s, will automate the export of sections of a
waveform channel, based around a trigger channel, to individual Matlab files. The
script allows the user to set the trigger channel and source waveform along with
a time range of data to export. The exported sections of data are saved to the
same folder location with the same filename as the original file and a suffix
indicating the count of the sections exported. The files also include a TextMark
channel with a marker holding the trigger time from the original file.
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Right-click the script icon
and save to disk.
If you have any problems
opening the embedded
scripts in this newsletter
please let us know.
The script requires Spike2 version 6 or higher. It could also be modified to export
triggered data to other file formats if required.
Q.
I’d be interested to know which models are supported by the dynamic clamp
system in Signal. In the past I have used a “home grown” system but the
programmer from our group has now left and so we no longer have any support
for our existing set-up.
A.
The Dynamic Clamp system in Signal is configured from the Clamp tab of the
sampling configuration dialog. The clamp section of the sampling configuration
can be enabled or disabled from the Clamp tab of the Edit menu
Preferences dialog and provides the main setup dialog which is used to define
the models to use during an experiment. This dialog can be accessed on-line to
enable or disable models and to view, edit and update model parameters while
sampling. Up to 15 models of any type can be defined for use on-line in a single
sampling configuration. The number of models that are able to run
simultaneously during sampling is dependent on the sample rate and model
complexity.
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Adding models to the Dynamic clamp setup
Below is a data file showing action potentials simulated using the combination of
models in the setup dialog above.
Simulated action potentials
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Hodgkin-Huxley
These models are used to simulate the membrane conductance generated by a
population of voltage-dependent ion channels that obey the standard HodgkinHuxley equations:
•
Hodgkin-Huxley (Alpha/Beta)- uses a formulation based upon multiple
rate equations
•
Hodgkin-Huxley (Tau)- uses a formulation based on thresholds and
threshold sensitivities
Synapse
These are used to simulate synaptic current flow between two cells:
•
Alpha synapse- uses the Alpha function to generate the post-synaptic
conductance profile
•
CPG synapse- the pre-synaptic potential mediates the release of a
transmitter which causes a post-synaptic current to flow. This particular
model mimics the behaviour of synapses in the central pattern
generation region of the lobster central nervous system
•
Destexhe synapse- uses the Destexhe model to generate the postsynaptic conductance profile. The synapse can be activated by the presynaptic potential being above or below a defined threshold
•
Electrical synapse- simulates a simple electrical connection (a gap
junction) between two cells
•
Exponential synapse- simulates the presence of a synapse using an
instantaneous rise time and a single exponential to mimic the post-trigger
decay of the conductance
•
Exponential difference synapse- generates the post-synaptic
conductance profile based on the difference between two exponentials,
one used to model the rising phase and the other to model the decay
•
User-defined synapse- generates a post-synaptic conductance based
on a user-defined waveform read from a text file
Leak models
These provide simpler dynamic clamp behaviours where the simulated
conductance is not time-dependent:
•
Linear leak- represents current leakage through a cell membrane with
constant conductance
•
Goldmann-Hodgkin-Katz (GHK) leak- simulates the behaviour caused
by diffusion of an ion through a membrane via always-open ion channels,
driven by the differing ionic concentrations either side of the membrane
and the voltage difference across it
•
Boltzmann leak- resembles a linear leak with an additional factor in the
equation that represents a voltage-dependent blockage of the leak
Noise
This model can be used to study the effect of simulated noisy conductances on
neuronal behaviour:
•
Ornstein-Uhelenbeck noise- generates a noise model using the mean
reverting stochastic process
Full details of the available models, and the mathematics used to generate them,
is available in the Signal on-line help.
Scripts: Signal
Q.
I have been using the script, IntraSpikeAnalysis.sgs, which was included
in eNewsletter 58, to take automated measurements from action potentials. This
works fine, but would it be possible to extend the script to give the half-height of
each spike as well?
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Right-click the script icon
and save to disk.
If you have any problems
opening the embedded
scripts in this newsletter
please let us know.
A.
The script, IntraSpikeAnalysis v2.sgs, has been extended from the
original version to include a measurement of the spike half-height alongside the
standard measurements, which are then printed to a text file. This script requires
Signal version 4 or higher.
Did you know…?
You can display channels in any order in a data or result file by clicking on the channel
number to the left of the Y-axis and dragging it to a new position.
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Recent questions
Q.
I am currently using Signal, a Micro1401 and a 1902 along with a Magstim 2002
stimulator for experiments investigating cortical processing of speech sounds. I’m
recording EMG from a lip electrode but find that the TMS pulse introduces a large
artefact which makes measurement of the responses difficult. I am intending to
use the 1902 input clamp option to counter the artefact but would like to know if it
is possible to trigger the input clamp slightly before the TMS pulse occurs?
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A.
The input clamp option of the 1902 should always be activated before the
stimulator for optimal results. It can be triggered by either the rising or falling
edge of a TTL pulse delivered to the Trigger 2 input socket on the front panel.
You can set which edge of a pulse to use in the 1902 controls dialog. By
default the input clamp is set to use the rising edge of a pulse.
1902 control dialog with input clamp setting of 5ms
2
The Magstim range can also be set to trigger on either the rising or falling edge
of a pulse by wiring the trigger signal to the appropriate pin on the 26-way
connector on the rear of the unit (pin 5 = rising edge, pin 6= falling edge). In this
way you could use a single 1401 digital output wired to both Trigger 2 on the
1902 and pin 6 of the Magstim unit to trigger the input clamp on the rising edge of
the pulse and the stimulator on the falling edge, giving a suitable delay between
clamp and stimulus.
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